Hostname: page-component-78c5997874-lj6df Total loading time: 0 Render date: 2024-11-10T06:19:20.542Z Has data issue: false hasContentIssue false
  • English
  • Français

Contemporary methods to investigate seed and bud dormancy

Published online by Cambridge University Press:  20 January 2017

Wun S. Chao
Wun S. Chao*
Affiliation:
USDA—Agricultural Research Service, Plant Science Research, Biosciences Research Laboratory, Fargo, ND 58105-5674; chaow@fargo.ars.usda.gov
Get access Rights & Permissions [Opens in a new window]

Abstract

Dormancy is a state of shifted physiological activities with cessation of growth. It occurs in seeds and vegetative propagules and enables plants to survive in adverse growing conditions. Traditional studies on dormancy-related problems have mostly focused on hormone changes along with environmental factors that have achieved great insight on these processes at the physiological level. The molecular nature and cellular basis of signals that carry out the processes of dormancy or dormancy breaking are largely unknown. Recent advances in plant genetics and genomics have provided assorted ways to investigate questions concerning dormancy. Various approaches such as developing genetic maps with DNA-based markers, e.g., amplified fragment length polymorphism (AFLP) and restriction fragment length polymorphism (RFLP), analyzing mutant lines, conducting quantitative trait loci (QTL) analysis, two-dimensional polyacrylamide gel electrophoresis, differential display, microarray, have been performed to resolve different issues related to dormancy. The phenotypic variation in dormant seeds or buds is continuous instead of discrete, and thus QTL analysis is desirable to identify the association between genetically determined phenotypes and specific genetic markers (RFLPs). Some aspects of QTL will be introduced. DNA microarray is a recently developed technology that is used to detect and quantitate large numbers of differences in gene expression simultaneously. We have used the DNA microarray technology to study underground bud dormancy and growth in leafy spurge (Euphorbia esula L.). The principle and versatility of DNA microarray will be introduced, and the strategy for applying this technology will be discussed.

Keywords

Leafy spurge, Euphorbia esula L. EPHESGenomicsdormancymicroarrayquantitative trait locivirus-induced gene silencing
Type
Research Article
Information
Weed Science , Volume 50 , Issue 2 , April 2002 , pp. 215 - 226
Copyright
Copyright © Weed Science Society of America 

Access options

Get access to the full version of this content by using one of the access options below. (Log in options will check for institutional or personal access. Content may require purchase if you do not have access.)

References

Literature Cited

Aharoni, A., Keizer, L.C.P., Bouwmeester, H. J. et al. 2000. Identification of the SAAT gene involved in strawberry flavor biogenesis by use of DNA microarrays. Plant Cell 12:647–661.Google Scholar
Alpert, K. B. and Tanksley, S. D. 1996. High-resolution mapping and isolation of a yeast artificial chromosome contig containing fw2.2: a major fruit weight quantitative trait locus in tomato. Proc. Natl. Acad. Sci. USA 93:15 503–15 507.Google Scholar
Anandalakshmi, R., Pruss, G. J., Ge, X., Marathe, R., Smith, T. H., and Vance, V. B. 1998. A viral suppressor of gene silencing in plants. Proc. Natl. Acad. Sci. USA 95:13 079–13 084.CrossRefGoogle ScholarPubMed
Anderson, J. V., Chao, W. S., and Horvath, D. P. 2001. A current review on the regulation of dormancy in vegetative buds. Weed Sci. 49:581–589.Google Scholar
Ausubel, F. M. 2000. Arabidopsis genome. A milestone in plant biology. Plant Physiol. 124:1451–1454.Google Scholar
Baulcombe, D. C. 1999. Fast forward genetics based on virus-induced gene silencing. Curr. Opin. Plant Biol. 2:109–113.CrossRefGoogle ScholarPubMed
Baulcombe, D. C., Chapman, S., and Santa Cruz, S. 1995. Jellyfish green fluorescent protein as a reporter for virus infections. Plant J. 7:1045–1053.Google Scholar
Brown, S. M. and Kresovich, S. 1996. Molecular characterization for plant genetic resources conservation. Pages 86–93 In Patterson, A. H., ed. Genome Mapping in Plants. Austin: Academic Press/R. G. Landes.Google Scholar
Buchanan, B. B., Gruissem, W., and Jones, R. L. 2000. Biochemistry & Molecular Biology of Plants. Rockville, MD: American Society of Plant Physiologists. pp. 260–310.Google Scholar
Burton, R. A., Gibeaut, D. M., Bacic, A., Findlay, K., Roberts, K., Hamilton, A., Baulcombe, D. C., and Fincher, G. B. 2000. Virus-induced silencing of a plant cellulose synthase gene. Plant Cell 12:691–705.CrossRefGoogle ScholarPubMed
Cogoni, C. and Macino, G. 2000. Post-transcriptional gene silencing across kingdoms. Curr. Opin. Genet. Dev. 10:638–643.CrossRefGoogle ScholarPubMed
Dalmay, T., Hamilton, A., Mueller, E., and Baulcombe, D. C. 2000a. Potato virus X amplicons in Arabidopsis mediate genetic and epigenetic gene silencing. Plant Cell 12:369–379.Google Scholar
Dalmay, T., Hamilton, A., Rudd, S., Angell, S., and Baulcombe, D. C. 2000b. An RNA-dependent RNA polymerase gene in Arabidopsis is required for posttranscriptional gene silencing mediated by a transgene but not by a virus. Cell 101:543–553.CrossRefGoogle Scholar
Duggan, D. J., Bittner, M., Chen, Y., Meltzer, P., and Trent, J. M. 1999. Expression profiling using cDNA microarrays. Nat. Genet. Suppl. 21:10–14.Google Scholar
Dutt, M. J. and Lee, K. H. 2000. Proteomic analysis. Curr. Opin. Biotechnol. 11:176–179.CrossRefGoogle ScholarPubMed
Edwards, M. D., Stuber, C. W., and Wendel, J. F. 1987. Molecular-marker-facilitated investigations of quantitative-trait loci in maize. I. Numbers, genomic distribution and types of gene action. Genetics 116:113–125.Google Scholar
Eisen, M. B., Spellman, P. T., Brown, P. O., and Botstein, D. 1998. Cluster analysis and display of genome-wide expression patterns. Proc. Natl. Acad. Sci. USA 95:14 863–14 868.Google Scholar
Epstein, C. B. and Butow, R. A. 2000. Microarray technology-enhanced versatility, persistent challenge. Curr. Opin. Biotechnol. 11:36–41.CrossRefGoogle ScholarPubMed
Fischer, R., Vaquero-Martin, C., Sack, M., Drossard, J., Emans, N., and Commandeur, U. 1999. Toward molecular farming in the future: transient protein expression in plants. Biotechnol. Appl. Biochem. 30:113–116.Google Scholar
Foder, S. P. A., Read, J. L., Pirrung, M. C., Stryer, L., Lu, A. T., and Solas, D. 1991. Light-directed, spatially addressable parallel chemical synthesis. Science 251:767–773.Google Scholar
Foley, M. E. 2001. Seed dormancy: an update on terminology, physiological genetics, and quantitative trait loci regulating germinability. Weed Sci. 49:305–317.Google Scholar
Frary, A., Nesbitt, T. C., Frary, A. et al. 2000. fw2.2: a quantitative trait locus key to the evolution of tomato fruit size. Science 289:85–88.CrossRefGoogle Scholar
Frewen, B. E., Chen, T. H. H., Howe, G. T., Davis, J., Rohde, A., Boerjan, W., and Bradshaw, H. D. Jr. 2000. Quantitative trait loci and candidate gene mapping of bud set and bud fluch in Populus. Genetics 154:837–845.Google Scholar
Goodwin, J., Chapman, K., Swaney, S., Parks, T. D., Wernsman, E. A., and Dougherty, W. G. 1996. Genetic and biochemical dissection of transgenic RNA-mediated virus resistance. Plant Cell 8:95–105.Google Scholar
Gygi, S. P., Rochon, Y., Franza, B. R., and Aebersold, R. 1999. Correlation between protein and mRNA abundance in yeast. Mol. Cell. Biol. 19:1720–1730.Google Scholar
Hamilton, A. and Baulcombe, D. C. 1999. A species of small antisense RNA in posttranscriptional gene silencing in plants. Science 286:950–952.Google Scholar
Hess, D., Anderson, R. J., and Reagan, J. D. 2001. High throughput synthesis and screening: the partner of genomics for discovery of new chemicals for agriculture. Weed Sci. 49:249–256.CrossRefGoogle Scholar
Hutvágner, G., Mlynárová, L., and Nap, J.- P. 2000. Detailed characterization of the posttranscriptional gene-silencing-related small RNA in a GUS gene-silenced tobacco. RNA 6:1445–1454.Google Scholar
Jones, N., Ougham, H., and Thomas, H. 1997. Markers and mapping: we are all geneticists now. In Thomas, H. and Farrar, J. F., eds. Putting Plant Physiology on the Map: Genetic Analysis of Developmental and Adaptive Traits. Cambridge: Cambridge University Press. [See also New Phytol. 137:165–177.]Google Scholar
Kasschau, K. D. and Carrington, J. C. 1998. A counter-defensive strategy of plant viruses: suppression of post-transcriptional gene silencing. Cell 95:461–470.Google Scholar
Kearsey, M. J. and Pooni, H. S. 1996. The Genetical Analysis of Quantitative Traits. London: Chapman and Hall. pp. 133–164.CrossRefGoogle Scholar
Kjemtrup, S., Sampson, K. S., Peele, C. G., Nguyen, L. V., Conkling, M. A., Thompson, W. F., and Robertson, D. 1998. Gene silencing from plant DNA carried by a geminivirus. Plant J. 14:91–100.CrossRefGoogle ScholarPubMed
Kumagai, M. H., Donson, J., Della-Cioppa, G., Harvey, D., Hanley, K., and Grill, L. K. 1995. Cytoplasmic inhibition of carotenoid biosynthesis with virus-derived RNA. Proc. Natl. Acad. Sci. USA 92:1679–1683.CrossRefGoogle ScholarPubMed
Krysan, P. J., Young, J. C., and Sussman, M. R. 1999. T-DNA as an insertional mutagen in Arabidopsis . Plant Cell 11:2283–2290.Google Scholar
Lander, E. S. and Botstein, D. 1989. Mapping Mendelian factors underlying quantitative traits using RFLP linkage maps. Genetics 121:185–189.CrossRefGoogle ScholarPubMed
Lewin, B. 1997. Genes VI. Oxford: Oxford University Press. pp. 49–237.Google Scholar
Li, F., Barnathan, E. S., and Kariko, K. 1994. Rapid method for screening and cloning cDNAs generated in differential messenger RNA display and application of northern blot for affinity capture of cDNAs. Nucleic Acids Res. 22:1764–1765.Google Scholar
Liang, P. and Pardee, A. B. 1992. Differential display of eukaryotic messenger RNA by means of the polymerase chain reaction. Science 257:967–971.CrossRefGoogle ScholarPubMed
Liang, P. and Pardee, A. B. 1995. Recent advances in differential display. Curr. Opin. Immunol. 7:247–280.Google Scholar
Lincoln, S., Daly, M., and Lander, E. 1993. Mapping Genes Controlling Quantitative Traits with MAPMAKER/QTL 1.1: A Tutorial and Reference Manual. Whitehead Institute Technical Report.Google Scholar
Lindbo, J. A. and Dougherty, W. G. 1992. Untranslatable transcripts of the tobacco etch virus coat protein gene sequence can interfere with tobacco etch virus replication in transgenic plants and protoplasts. Virology 189:725–733.Google Scholar
Matzke, M. A., Mette, M. F., and Matzke, A. J. M. 2000. Transgene silencing by the host genome defense: implications for the evolution of epigenetic control mechanisms in plants and vertebrates. Plant Mol. Biol. 43:401–415.Google Scholar
Nelson, J. C. 1997. QGENE: software for marker-based genomic analysis and breeding. Mol. Breed. 3:239–245.Google Scholar
Paterson, A. H. 1996a. Making genetic maps. Pages 23–39 In Patterson, A. H., ed. Genome Mapping in Plants. Austin: Academic Press/R. G. Landes.Google Scholar
Paterson, A. H. 1996b. Mapping genes responsible for differences in phenotype. Pages 41–54 In Patterson, A. H., ed. Genome Mapping in Plants. Austin: Academic Press/R. G. Landes.Google Scholar
Paterson, A. H., Schertz, K. F., Lin, Y.-R., Liu, S.-C., and Chang, Y.- L. 1995. The weediness of wild plants: molecular analysis of genes influencing dispersal and persistence of johnsongrass, Sorghum halepense (L.) Pers. Proc. Natl. Acad. Sci. USA 92:6127–6131.Google Scholar
Ratcliff, F., Harrison, B. D., and Baulcombe, D. C. 1997. A similarity between viral defense and gene silencing in plants. Science 276:1558–1560.Google Scholar
Reymond, P., Weber, H., Damond, M., and Farmer, E. E. 2000. Differential gene expression in response to mechanical wounding and insect feeding in Arabidopsis . Plant Cell 12:707–719.Google Scholar
Rothschild, M. F. and Soller, M. 1997. Candidate gene analysis to detect genes controlling traits of economic importance in domestic livestock. Probe 8:13–20.Google Scholar
Ruiz, M. T., Voinnet, O., and Baulcombe, D. C. 1998. Initiation and maintenance of virus-induced gene silencing. Plant Cell 10:937–946.CrossRefGoogle ScholarPubMed
Sambrook, J., Fritsch, E. F., and Maniatis, T. 1989. Molecular Cloning: A Laboratory Manual. 2nd ed. New York: Cold Spring Harbor Laboratory Press.Google Scholar
Schena, M., Shalon, D., Davis, R. W., and Brown, P. O. 1995. Quantitative monitoring of gene expression patterns with a complementary DNA microarray. Science 270:467–470.Google Scholar
Springer, P. S. 2000. Gene traps: tools for plant development and genomics. Plant Cell 12:1007–1020.Google Scholar
Stansfield, W. D. 1991. Schaum's Outline of Theory and Problems of Genetics. 3rd ed. Schaum's Outline Series. New York: McGraw-Hill. pp. 209–212.Google Scholar
Stevenson, B. J. 1999. Available: LICR Office of Information Technology, http://epd.unil.ch/biocomputing/array/software/MicroArray_Software.htm.Google Scholar
Sun, Y., Hegamyer, G., and Colburn, N. H. 1994. Molecular cloning of 5 messenger RNAs differentially expressed in preneoplastic or neoplastic JB6 mouse epidermal cells—one which is homologous to human tissue inhibitor of metalloproteinase 3. Cancer Res. 54:1139–1144.Google Scholar
Tanksley, S. D., Ganal, M. W., and Martin, G. B. 1995. Chromosome landing: a paradigm for map-based gene cloning in plants with large genomes. Trends Genet. 11:63–68.CrossRefGoogle ScholarPubMed
Tautz, D. 1989. Hypervariability of simple sequences as a general source for polymorphic DNA markers. Nucleic Acids Res. 17:6463–6471.Google Scholar
Tavazoie, S., Hugues, J. D., Campbell, M. J., Cho, R. J., and Church, G. M. 1999. Systematic determination of genetic network architecture. Nat. Genet. 22:281–285.Google Scholar
van Hal, N. L. W., Vorst, O., van Houwelingen, A. M. M. L., Kok, E. J., Peijnenburg, A., Aharoni, A., van Tunen, A. J., and Keijer, J. 2000. The application of microarrays in gene expression analysis. J. Biotechnol. 78:271–280.Google Scholar
Veculescu, V. E., Zhang, L., Vogelstein, B., and Kinzler, K. W. 1995. Serial analysis of gene expression. Science 270:484–487.Google Scholar
Verch, T., Yusibov, V., and Koprowski, H. 1998. Expression and assembly of a full-length monoclonal antibody in plants using a plant virus vector. J. Immunol. Methods 220:69–75.CrossRefGoogle ScholarPubMed
Waterhouse, P. M., Graham, M. W., and Wang, M.- B. 1998. Virus resistance and gene silencing in plants can be induced by simultaneous expression of sense and antisense RNA. Proc. Natl. Acad. Sci. USA 95:13 959–13 964.Google Scholar
Waterhouse, P. M., Smith, N. A., and Wang, M.- B. 1999. Virus resistance and gene silencing: killing the messenger. Trends Plant Sci. 4:452–457.Google Scholar
Wen, X., Fuhrman, S., Michaels, G. S., Carr, D. B., Smith, S., Barker, J. L., and Somogyi, R. 1998. Large-scale temporal gene expression mapping of central nervous system development. Proc. Natl. Acad. Sci. USA 95:334–339.CrossRefGoogle ScholarPubMed
Williams, J. G., Kubelik, A. R., Livak, K. J., Rafalski, J. A., and Tingey, S. V. 1990. DNA polymorphisms amplified by arbitrary primers are useful as genetic markers. Nucleic Acids Res. 18:6531–6535.Google Scholar
Yang, D., Lu, H., and Erickson, J. W. 2000. Evidence that processed small dsRNSs may mediate sequence-specific mRNA degradation during RNAi in Drosophila embryos. Curr. Biol. 10:1191–1200.Google Scholar
Zabeau, M. and Vos, P., inventors. 1993. Selective restriction fragment amplification: a general method for DNA fingerprinting. EPO Patent 0534858A1.Google Scholar